Locus 5212

Sequence ID dm3.chr2R
Location 18,569,436 – 18,569,575
Length 139
Max. P 0.850225
window7150 window7151

overview

Window 0

Location 18,569,436 – 18,569,536
Length 100
Sequences 7
Columns 123
Reading direction forward
Mean pairwise identity 66.68
Shannon entropy 0.56449
G+C content 0.54039
Mean single sequence MFE -36.60
Consensus MFE -16.53
Energy contribution -17.51
Covariance contribution 0.99
Combinations/Pair 1.40
Mean z-score -1.62
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.91
SVM RNA-class probability 0.850225
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18569436 100 + 21146708
----------------------CUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCC
----------------------.(((((..((.....((((..(..((.........))..)..)))).(((((((((((-(((....)))))))))....))))))).)))))......... ( -38.80, z-score =  -1.56, R)
>droSim1.chr2R 17163382 94 + 19596830
----------------------CUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCU-------CUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCC
----------------------.(((((..(((....((((..(..((.........))..)..))))(((((((((.-------...)))))))))........))).)))))......... ( -36.00, z-score =  -1.76, R)
>droSec1.super_9 1871671 100 + 3197100
----------------------CUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCC
----------------------.(((((..((.....((((..(..((.........))..)..)))).(((((((((((-(((....)))))))))....))))))).)))))......... ( -38.80, z-score =  -1.56, R)
>droYak2.chr2R 16034595 101 + 21139217
----------------------CUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUUGGUGGUGCUACAGCUACAGCUACGAGUUCUAGCUGCGGCUAAUGGUGGUGCCUCGCAUAUCCUUUC
----------------------.(((((..(((....((((..(..((.........))..)..))))(((..((((((.(....)))))))..)))........))).)))))......... ( -35.10, z-score =  -0.76, R)
>droEre2.scaffold_4845 19929401 100 + 22589142
----------------------CCACGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCG
----------------------.(((((..((((.........)))).)))))...(((.((..(((((((((((((((.-.....)))))))))))....))))..)))))........... ( -37.10, z-score =  -1.17, R)
>droVir3.scaffold_12875 13779470 111 + 20611582
CUGCCCUUUGACACUGACAAGGAUGAGGAUGCCG-UGCCGCUGCUGCUCCUCGUCCUGGGCCUGUUACAGCUUC-GCUGUGA----UAACCUUGCC--GCGGUGGUGCUUUAUCAAAUU----
...........(((((.(.((((((((((.((.(-(......)).)))))))))))).(((.(((((((((...-)))))))----)).....)))--))))))...............---- ( -39.50, z-score =  -2.21, R)
>droGri2.scaffold_15245 861771 95 - 18325388
CUGCCCUUUGA------------UGAGGAUGCC--UACUCCUGCUGCUGCUG---UUGCGGCUGCUUCAGCUCC-GCUGUGA----UAACCUUGCC--GCGGUGGUGCUUUAUUAAAUU----
......(((((------------((((((....--...))).((.(((((..---..))))).))...(((.((-((((((.----.........)--))))))).)))))))))))..---- ( -30.90, z-score =  -2.33, R)
>consensus
______________________CUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC_AG_UCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCC
.......................(((((..((((.........)))).)))))...(((.((((((((((((.((((((.......)))))).))))....)))))))))))........... (-16.53 = -17.51 +   0.99)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 18,569,461 – 18,569,575
Length 114
Sequences 7
Columns 122
Reading direction forward
Mean pairwise identity 76.54
Shannon entropy 0.42433
G+C content 0.50704
Mean single sequence MFE -37.11
Consensus MFE -23.00
Energy contribution -25.04
Covariance contribution 2.04
Combinations/Pair 1.23
Mean z-score -1.28
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.21
SVM RNA-class probability 0.595911
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18569461 114 + 21146708
------UUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCAUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU-
------...(..((((((.((..(((((((((((((((.-.....)))))))))))....))))..)).)......((.((((.((...)).)))).))......)))))..)........- ( -40.40, z-score =  -1.67, R)
>droSim1.chr2R 17163407 108 + 19596830
------UUUGUGUUUCGGUGGUGCUACAGCUACAG-------CUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU-
------...(..((((((.((..((((((((((((-------(....)))))))))....))))..)).)......((.(((..((...))..))).))......)))))..)........- ( -37.70, z-score =  -1.81, R)
>droSec1.super_9 1871696 114 + 3197100
------UUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU-
------...(..(((((..(((((((((((((.(((...-.))).))))))).(((...((((((((...))))..((......)).))))...)))))))))..)))))..)........- ( -40.30, z-score =  -1.81, R)
>droYak2.chr2R 16034620 115 + 21139217
------UUUGUGUUUUGGUGGUGCUACAGCUACAGCUACGAGUUCUAGCUGCGGCUAAUGGUGGUGCCUCGCAUAUCCUUUCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU-
------...(..(((((..(((((..((((((.(((.....))).))))))((.((((.((((((((...))))..((......)).)))))))).)))))))..)))))..)........- ( -34.70, z-score =  -0.18, R)
>droEre2.scaffold_4845 19929426 114 + 22589142
------UUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCGUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU-
------..........((.((..(((((((((((((((.-.....)))))))))))....))))..))..((((((..(((((..(((.((...)).)))....)))))))))))..))..- ( -40.70, z-score =  -1.87, R)
>droVir3.scaffold_12875 13779510 111 + 20611582
UGCUGCUCCUCGUCCUGGGCCUGUUACAGCUUCGCU-----GUGAUAACCUUGCC--GCGGUGGUGCUU----UAUCAAAUUCUGGUCACCUUGGGCGGCAUUUACAAAAUGUGUAUCCACU
((((((((.((((...(((..(((((((((...)))-----)))))).)))....--)))).((((((.----...........)).))))..))))))))..........(((....))). ( -32.70, z-score =  -0.88, R)
>droGri2.scaffold_15245 861795 111 - 18325388
UCCUGCUGCUGCUGUUGCGGCUGCUUCAGCUCCGCU-----GUGAUAACCUUGCC--GCGGUGGUGCUU----UAUUAAAUUCUGGUCACCUUGGGCAGCAUUUACAAAAUGUGUAUCCACU
....((.(((((....))))).))...(((.(((((-----(((..........)--))))))).))).----...(((((.(((.((.....)).))).)))))......(((....))). ( -33.30, z-score =  -0.73, R)
>consensus
______UUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC_AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAU_
...........((((((.....((((((((((.(((.....))).))))))))))....((((.(((((.......((......)).......))))).))))..))))))........... (-23.00 = -25.04 +   2.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:58 2011